I split it between the three. Magic, Health, Stamina. But if I drop all my perks into one thing the other two would be very low and I'd be a one hit kill correct?
Hard to say.. it's a balance between the three depending on the type of character you're playing. There are a number of ways to boost your carrying capacity without having to sacrifice health and/or magicka. Deep Pockets on the pickpocketing tree gives you an extra 100 capacity. The steed stone gives you another 100. The higher perks on the armor trees also allow the weight of the armor you're wearing to be 0 with a full set (chest, arms, feet, head). I've found that around 500 is easily doable, and can haul all of the stuff you need to carry.
Always remember, you don't need to pick up every single item in a dungeon. Balance out whether or not it's cost effective to carry that much weight. An iron warhammer for instance, won't net you much gold and should be overlooked, while an ebony warhammer will net a nice sum at sale. But, you have to decide what to pass over and not.
I usually leave anything that's less than 100gp behind. It's not worth me bogging down my inventory with them. Many times however, I will pick up items, get to my weight limit, then decide what's the least expensive item to leave behind. It pains me sometimes, but gold in Skyrim is easy enough to come by.